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01.
arXiv (CS.AI) 2026-06-17

Breaking the Code: Security Assessment of AI Code Agents Through Systematic Jailbreaking Attacks

arXiv:2510.01359v2 Announce Type: replace-cross Abstract: Code-capable large language model (LLM) agents are embedded in software engineering workflows where they can read, write, and execute code, raising "jailbreak" stakes beyond text-only settings. Prior evaluations emphasize refusal or harmful-text detection, leaving open whether agents compile and run malicious programs. We present JAWS-Bench (Jailbreaks Across WorkSpaces), a benchmark spanning three escalating workspace regimes mirroring attacker capability: empty (JAWS-0), single-file (JAWS-1), and multi-file (JAWS-M). We pair this with a hierarchical, executable-aware Judge Framework that tests (i) compliance, (ii) attack success, (iii) syntactic correctness, and (iv) runtime executability, to measure deployable harm. Across seven LLM backends from five families, prompt-only attacks in JAWS-0 achieve 61% compliance; 58% are harmful, 52% parse, and 27% run end-to-end. In JAWS-1, compliance reaches ~100% for stronger models with a mean ASR (Attack Success Rate) ~71%; JAWS-M raises mean ASR to ~75%, with 32% runnable attack code. Wrapping an LLM in an agent increases ASR by 1.6$\times$, by overturning initial refusals during planning and tool use. Similar trends hold for OpenHands, SWE-Agent, and OpenAI Codex, suggesting our JAWS-Bench is agent-agnostic. Category analyses identify which attack classes are most vulnerable and deployable, motivating execution-aware defenses and refusal-preserving agent designs.

02.
medRxiv (Medicine) 2026-06-17

Multi-strain Probiotics Alter Gut Microbiota and Estrobolome Pathways in Primary Dysmenorrhea

Background: Exact cause of primary dysmenorrhoea is unknown but recent evidence uncovers a potential link between gut dysbiosis and benign gynaecological disorder via disruption of estrobolome. Methods: A randomized controlled trial to investigate the effects of multi-strain oral probiotics on primary dysmenorrhoea has been conducted. This is a secondary analysis comparing the stool microbiome in women with primary dysmenorrhoea and those without (control), and the effects of treatment with probiotics versus placebo. Results: Although microbial richness and evenness were comparable between groups (alpha diversity, p > 0.05), gut microbial community composition differed significantly (Bray Curtis PERMANOVA, p = 0.015), characterised by reduced Bifidobacterium adolescentis and Blautia and enrichment of Faecalibacterium in dysmenorrhoea, alongside condition-specific core taxa. Post-intervention analysis revealed significant shifts in microbial community structure between pre- and post-treatment groups (PERMANOVA, F = 2.11, p = 0.005), with probiotic supplementation inducing more consistent and directed microbiome changes than placebo, without altering alpha diversity (p > 0.05). Functional prediction showed no significant difference in overall beta glucuronidase pathway abundance (p > 0.05); however, dysmenorrhoea was associated with higher abundance of beta glucuronidase producing taxa (MaAsLin2, q < 0.05) that were differentially modulated by probiotic treatment. Conclusion: This discovery provides evidence on the microbial disruption in primary dysmenorrhoea as well as the benefit of probiotics to modulate the intestinal microbiota to improve the condition.

03.
arXiv (CS.CV) 2026-06-12

VideoMDM: Towards 3D Human Motion Generation From 2D Supervision

We introduce VideoMDM, a diffusion-based framework that trains 3D human motion priors directly from accurate 2D poses extracted from monocular videos, without any 3D ground truth. A pretrained 2D-to-3D lifter provides approximate 3D pose sequences that serve as a noisy teacher: these are diffused, denoised by the model in 3D, and supervised in 2D by reprojecting the prediction and comparing against accurate keypoints. We show that, under mild assumptions, a depth-weighted 2D reprojection loss is equivalent in expectation to direct 3D supervision, and we adapt standard 3D motion regularizers - velocity consistency and over-parameterized representation alignment - to this 2D setting. Unlike methods that lift 2D to 3D only at inference, VideoMDM learns a coherent 3D motion manifold during training. On HumanML3D it nearly closes the gap to fully 3D-supervised MDM (FID 0.88 vs 0.54); On real video datasets Fit3D and NBA the method learns to generate motions consistently preferred by humans, with strong quantitative results.

04.
arXiv (CS.CL) 2026-06-17

Scaling Enterprise Agent Routing: Degradation, Diagnosis, and Recovery

Production LLM assistants route user requests to growing libraries of specialized tools, but how does routing accuracy degrade as the catalog scales? We study single-step routing on a 110-agent, 584-tool catalog from a deployed enterprise productivity assistant, evaluating three frontier models from 10 to 110 agents. Routing F1 on under-specified requests drops 16–23 percentage points across models. An oracle analysis decomposes the degradation into a retrieval gap (the model cannot surface the right tool) and a confusion gap (even with perfect retrieval, the oracle ceiling drops 10pp). Embedding-based shortlisting recovers +10–11pp F1 at full scale across all three models and two providers. A production annotation study (1,435 human-labeled utterances, three annotators) confirms the recovery on real traffic at +10–17pp despite 10–15pp lower absolute performance.

05.
arXiv (CS.CL) 2026-06-12

Observable Patterns Are Not Explanations: A Causal-Geometric Analysis of Latent Reasoning Models

Latent reasoning models (LRMs) replace explicit chain-of-thought with continuous thoughts. Recent work treats observable latent-state patterns, such as BFS-like frontiers and decodable arithmetic computation, as evidence for internal reasoning mechanisms. Evaluating two LRMs (Coconut and CODI) against controls lacking the proposed recurrence or curriculum, we find these patterns also appear in the controls and do not always causally affect behavior. Causal interventions reveal that latent-thought utilization is not binary but graded, scaling with a thought's causal effect on model behavior. Geometric analyses reveal this effect concentrates in low-rank directions whose step-to-step geometry grows more structured as their behavioral influence increases. Latent thoughts should therefore be treated as hidden computation, not hidden explanation: decodability, attention, or static structure alone cannot establish mechanism. LRM interpretability thus requires matched controls and causal tests.

06.
medRxiv (Medicine) 2026-06-22

AI-Assisted Longitudinal Analyses of Environmental and Psychosocial Determinants of Subjective Cognitive Difficulties

作者:

Short-term environmental exposures have been linked to cognitive and behavioral outcomes, although many reported associations may reflect broader geographic and contextual differences. Using longitudinal data from the All of Us Research Program (2018–2024), we linked daily weather and air-pollution exposures to repeated attention-related and subjective cognitive outcomes. Associations were evaluated using pooled, fixed-effects, lagged, and event-study analyses. Additional machine-learning analyses were conducted to explore potential heterogeneity and latent psychosocial structure. Replication analyses were performed using the 2024 Behavioral Risk Factor Surveillance System (BRFSS). Several environmental exposure measures showed small associations with cognitive outcomes in pooled analyses, but most attenuated substantially after accounting for within-location temporal variation. Mediation, sensitivity, and machine-learning analyses yielded similar conclusions. In contrast, mental-health burden, loneliness, and social functioning were consistently associated with subjective cognitive difficulty and exhibited substantially larger effect sizes than environmental exposures. Similar patterns were observed in BRFSS. Exploratory AI-assisted analyses yielded findings broadly consistent with the primary longitudinal analyses. These findings suggest that short-term environmental perturbations may have limited associations with cognitive outcomes after accounting for within-location variation, whereas psychosocial factors appear to be more consistently associated with subjective cognitive burden.

07.
arXiv (CS.LG) 2026-06-15

Mitigating Heterogeneity-Induced Drift in Hierarchical Sign-Based Federated Learning

arXiv:2602.02355v2 Announce Type: replace-cross Abstract: Hierarchical federated learning (HFL) is well suited for large-scale wireless and Internet of Things systems, where devices communicate with nearby edge servers before reaching the cloud. In these environments, uplink bandwidth and latency impose strict communication constraints, making aggressive gradient compression essential. One-bit sign-based stochastic gradient descent methods provide an attractive solution in flat federated settings, but their behavior in hierarchical edge–cloud architectures remains insufficiently understood, especially under inter-cluster data heterogeneity. To address this gap, we develop a sign-based HFL framework in which devices transmit binary stochastic-gradient signs to edge servers, edge servers apply majority voting, and the cloud periodically aggregates edge models. Our analysis reveals that inter-cluster heterogeneity induces a persistent bias term in the convergence bound, reflecting the drift of edge models toward local objectives. This term cannot be removed by increasing the number of training rounds or by tuning standard hyperparameters alone. We therefore propose \(\mathtt{DC-HierSignSGD}\), a drift-corrected sign-based HFL algorithm in which devices apply a cloud-assisted gradient correction before taking the sign. We show that this pre-sign correction mitigates the non-vanishing heterogeneity-induced bias while preserving binary device–edge communication during the repeated local sign-update steps. Experiments under severe inter-cluster heterogeneity demonstrate that \(\mathtt{DC-HierSignSGD}\) improves the stability and accuracy of sign-based HFL and achieves performance comparable to full-precision hierarchical SGD with substantially lower device–edge communication.

08.
arXiv (CS.AI) 2026-06-19

Analyzing the Narration Gap in LLM-Solver Loops

arXiv:2606.19588v1 Announce Type: new Abstract: Formal tools such as SAT and SMT solvers are increasingly embedded in language model reasoning pipelines when a safety or security critical question can be formulated in logic. Unlike chain of thought whose steps are sampled from the model distribution without formal guarantee, a solver produces a sound and independently verifiable answer. However, the soundness guarantee can be lost in the interaction between the solver and the model. The hybrid pipeline has three components: formalizing the question, deciding it, and narrating the result. Prior work has studied the formalization and decision, but not narration, which is the step that turns a formal tool's output into the user answer. To fill the narration gap, we first model the LLM-solver loop as a verified decision procedure. We further evaluate five open-sourced models under prompt injection, and we find certificate gating makes the solver verdict sound, while an adversary can invert a verified conclusion across phrasings and channels. We study the mitigation through hardened prompt that reduces injection significantly but cannot eliminate it and still suffers under adaptive attack. Combining the formal analysis and empirical studies, we show in the LLM-solver loop, robustness does not reach to the answer that the user finally reads.

09.
arXiv (CS.AI) 2026-06-12

CausalMoE: A Billion-Scale Multimodal Foundation Model for Granger Causal Discovery with Pattern-Routed Heterogeneous Experts

arXiv:2606.13024v1 Announce Type: cross Abstract: Granger Causal Discovery (GCD) is fundamental for analyzing temporal dependencies in complex systems. However, existing neural GCD methods predominantly rely on a "one-size-fits-all" paradigm, struggling to capture distribution shifts and dynamic regime changes inherent in real-world time series. This often leads to entangled representations and spurious causal graphs. In this paper, we propose CausalMoE, a billion-scale multimodal Granger causal foundation model that explicitly models patch-level heterogeneity. CausalMoE introduces a Pattern-Routed Mixture of Heterogeneous Experts, which dynamically identifies latent temporal patterns and routes patches to specialized domain experts, effectively decoupling regime-specific mechanisms from shared dynamics. To ensure interpretable graph recovery, we design a Causality-Aware Self-Attention mechanism operating across variables, yielding sparse Granger causal graphs via proximal optimization. Furthermore, CausalMoE is the first to integrate LLMs and VLMs to align numerical signals with textual and visual priors, regularizing causal estimation in complex scenarios. Extensive experiments demonstrate that CausalMoE establishes a new state-of-the-art on fully supervised benchmarks, while effectively generalizing to few-shot settings where traditional methods fail.

11.
arXiv (CS.CL) 2026-06-12

PolyAlign: Conditional Human-Distribution Alignment

Post-training methods such as supervised fine-tuning (SFT) and preference optimization typically align language models toward a single global assistant behavior. While effective for improving average helpfulness, this can suppress the natural variation of human responses across languages, tasks, and dialogue settings. We study this problem as conditional human-distribution alignment: models should match the human response distribution appropriate to the current interaction context, rather than a universal response style. We introduce PolyAlign, a distribution-aware alignment framework that organizes bilingual interaction data into bucket-specific human reference distributions defined by language, interaction track, response family, and length. PolyAlign combines Bucket-Aware SFT, which balances optimization across heterogeneous buckets, with Human-Distribution Preference Optimization (HDPO), which regularizes preference learning using critic-estimated distance to bucket-specific human support. Across a bilingual evaluation suite covering English and Chinese single- and multi-turn settings, PolyAlign improves conditional naturalness and distributional faithfulness while preserving competitive task utility. The results suggest that post-training should move beyond global alignment objectives toward interaction-aware alignment with human response distributions.

12.
arXiv (CS.AI) 2026-06-16

AlignCoder: Aligning Retrieval with Target Intent for Repository-Level Code Completion

arXiv:2601.19697v2 Announce Type: replace-cross Abstract: Repository-level code completion remains a challenging task for existing code large language models (code LLMs) due to their limited understanding of repository-specific context and domain knowledge. While retrieval-augmented generation (RAG) approaches have shown promise by retrieving relevant code snippets as cross-file context, they suffer from two fundamental problems: misalignment between the query and the target code in the retrieval process, and the inability of existing retrieval methods to effectively utilize the inference information. To address these challenges, we propose AlignCoder, a repository-level code completion framework that introduces a query enhancement mechanism and a reinforcement learning based retriever training method. Our approach generates multiple candidate completions to construct an enhanced query that bridges the semantic gap between the initial query and the target code. Additionally, we employ reinforcement learning to train an AlignRetriever that learns to leverage inference information in the enhanced query for more accurate retrieval. We evaluate AlignCoder on two widely-used benchmarks (CrossCodeEval and RepoEval) across five backbone code LLMs, demonstrating an 18.1% improvement in EM score compared to baselines on the CrossCodeEval benchmark. The results show that our framework achieves superior performance and exhibits high generalizability across various code LLMs and programming languages.

13.
arXiv (CS.LG) 2026-06-18

TimeLAVA: Learning-Agnostic Data Valuation for Time Series

arXiv:2606.18729v1 Announce Type: cross Abstract: Data valuation quantifies the intrinsic quality of individual samples to enable principled data curation, quality control, and robust learning. For time series in critical domains such as healthcare, finance, and industrial monitoring, effective valuation methods are essential yet fundamentally lacking. Existing approaches are either model-dependent, limiting their generalizability, or designed for i.i.d. data and thus fail to capture temporal dependencies, multi-scale patterns, and non-stationary dynamics inherent to sequential data. We introduce TimeLAVA, a learning-agnostic framework that values temporal segments by their marginal contribution to minimizing distributional discrepancy between evaluated and reference data. At its core is a novel Selective Wavelet-based Wasserstein discrepancy combining multi-scale wavelet transforms for temporal localization with unbalanced optimal transport for robustness to distributional shifts. Segment values are efficiently computed via sensitivity analysis without requiring model training and aggregated into point-wise scores. We provide theoretical guarantees linking valuation to model-agnostic generalization and prove bounded sensitivity to outlier contamination. Extensive experiments across anomaly detection, data pruning, and label noise detection demonstrate that TimeLAVA produces significantly more informative value scores than existing methods on diverse real-world datasets.

14.
arXiv (CS.AI) 2026-06-11

EKF-Based Depth Camera and Deep Learning Fusion for UAV-Person Distance Estimation and Following in SAR Operations

arXiv:2602.20958v2 Announce Type: replace-cross Abstract: Vision-based Unmanned Aerial Vehicles (UAVs) frameworks aid human search tasks by detecting and recognizing specific individuals, then tracking and following them while maintaining a safe distance. A key safety requirement for UAV following is the accurate estimation of the distance between camera and target object under real-world conditions, achieved by fusing multiple image modalities. As part of the system for automatic people detection and face recognition using deep learning, in this paper we present the fusion of depth camera measurements and monocular camera-to-body distance estimation for robust tracking and following. Deep learning based filtering of depth camera data and estimation of camera-to-body distance from a monocular camera are achieved with YOLO-pose, enabling real-time fusion of depth information using the Extended Kalman Filter (EKF) algorithm. The proposed subsystem, designed for use in drones, estimates and measures the distance between the depth camera and the human body keypoints, to maintain the safe distance between the drone and the human target. Our system provides an accurate estimated distance, which has been validated against motion capture ground truth data. The system has been tested in real time indoors, where it reduces the average errors, RMSE and standard deviations of distance estimation up to 15,3% in three tested scenarios. Based on the test results, the EKF fusion-based approach increases the depth detection range by reducing the errors outside the optimal depth camera working range. It also shows improved robustness and precision in challenging conditions, such as reflections and poor visibility, making it suitable for SAR.

15.
arXiv (quant-ph) 2026-06-16

Synthesizing Arbitrary Non-Hermitian Hamiltonian with Stochastic Floquet Engineering

arXiv:2606.15664v1 Announce Type: new Abstract: The conventional Floquet engineering scheme synthesizes a given target Hamiltonian with a deterministic temporal periodic driving field. In this work, we introduce the stochastic Floquet engineering scheme that can synthesize an arbitrary non-Hermitian target Hamiltonian using a time-periodic driving field with noisy amplitude. Our method is rooted in the Hermitian dynamics taking noise as a valuable quantum resource with no need for loss or gain in prior. We apply our method to engineer a cavity Hamiltonian with dissipative coupling between Fock states, and to prepare a given quantum state from a generally arbitrary quantum state. The stochastic Floqut engineering also provides a way to generate non-unitary quantum gates, which take advantage in certain tasks compared to unitary quantum computing, without the need for ancillae or state-dependent updating.

16.
arXiv (quant-ph) 2026-06-15

Dealing with locality in QAOA

arXiv:2606.14447v1 Announce Type: new Abstract: Shallow-depth QAOA on sparse, high-diameter MaxCut instances faces a locality bottleneck: at depth \(p\), local observables can depend only on a bounded neighborhood of the circuit interaction graph. We propose a transport-augmented QAOA that keeps the MaxCut cost Hamiltonian unchanged but enriches the mixer with optimized, unweighted shortcut couplings (scheduled \(XX+YY\)) to collapse the effective interaction-graph diameter. Using exact finite-depth support recursions, we relate optimal shortcut placement to bounded-diameter graph augmentation, and show in benchmarks that (unlike ma-QAOA) performance becomes effectively size-invariant once the diameter is reduced. For bipartite families (base diameter 4), reducing the interaction path to \(d=1\) raises the ensemble-averaged approximation ratio from 0.7378 (ma-QAOA) to 0.9767 at \(p=1\) (\(\sigma=0.0251\), nine system sizes); on random trees (base diameter 10), at \(p=2\) it improves from 0.9226 to 0.9997 (\(\sigma=0.0001\)).

17.
arXiv (CS.AI) 2026-06-12

Optimizing Appliance Scheduling for Solar Energy Management Using Metaheuristic Algorithms

arXiv:2606.13407v1 Announce Type: new Abstract: Renewable energy is essential for meeting future energy demands; however, solar energy generation, which occurs only during daylight hours often does not align with household consumption patterns. Appliances such as cookers, washing machines, and dryers are typically operated according to user preferred schedules rather than solar energy availability, creating a scheduling optimization problem. The objective is to determine optimal appliance start times to maximize renewable energy utilization while minimizing user inconvenience and adhering to system constraints. This paper presents a metaheuristic approach using Iterated Local Search (ILS) and Simulated Annealing (SA) to optimize appliance start times, while considering appliance operating durations, power consumption, inverter limit, battery state of charge constraints, and solar generation forecasts. Unlike most existing work, the scheduling is extended beyond a single day to accommodate unfinished tasks from previous days (spillover), ensuring operational continuity and enabling sequential operation across multiple days. Experimental results show that the sequential multi-day scheduling framework effectively manages system constraints while ensuring user convenience under exclusive solar generation. These findings also open opportunities for future research on multi-objective trade-offs between investment in equipment of various sizes, return on that investment, and user satisfaction.

18.
arXiv (quant-ph) 2026-06-12

Proper and improper mixed states serve as different prior beliefs for quantum state retrodiction

arXiv:2502.10030v2 Announce Type: replace Abstract: A mixed quantum state can be taken as capturing an unspecified form of ignorance; or as describing the lack of knowledge about the true pure state of the system ("proper mixture"); or as arising from entanglement with another system that has been disregarded ("improper mixture"). These different views yield identical density matrices and therefore identical predictions for future measurements. But when used as prior beliefs for inferring the past state from later observations ("retrodiction"), they lead to different updated beliefs. This is a purely quantum feature of Bayesian agency. Based on this observation, we establish a framework for retrodicting on any quantum belief and we prove a necessary and sufficient condition for the equivalence of beliefs. We also illustrate how these differences have operational consequences in quantum state recovery.

19.
bioRxiv (Bioinfo) 2026-06-11

Calibrated Uncertainty Quantification for Patient-Level AML Drug Sensitivity Prediction Using Split Conformal Prediction

Accurate prediction of ex vivo drug sensitivity in acute myeloid leukemia (AML) patients from transcriptomic data is a critical challenge for precision oncology. Existing computational approaches have explored uncertainty quantification in cancer drug response prediction primarily using cell line data, while patient-level AML models typically rely on heuristic confidence measures rather than statistically calibrated uncertainty estimates. Here, we present a framework applying split conformal prediction to patient-level AML drug response modeling using the BeatAML 2.0 cohort. We trained Elastic Net and XGBoost regressors on bulk RNA-seq gene expression profiles from 318 AML patients, analyzing 34,764 patient-drug observations across 122 compounds. Baseline models achieved median Pearson R values of 0.291 (Elastic Net) and 0.281 (XGBoost) across 122 drugs. Wrapping these models with split conformal prediction yielded well-calibrated prediction intervals across three confidence levels: empirical coverages of 81.4%, 90.7%, and 95.5% against nominal targets of 80%, 90%, and 95%, respectively. Analysis of prediction interval widths revealed substantial drug-class-specific uncertainty patterns, with HDAC and BCL-2 inhibitors exhibiting markedly higher uncertainty than MDM2 inhibitors, suggesting a potential association between transcriptomic predictability and drug mechanism of action, although several drug classes were represented by only a small number of compounds. Predictive uncertainty was not significantly associated with ELN2017 molecular risk classification (Kruskal-Wallis p=0.395) or NPM1 mutation status (p=0.788). These results demonstrate that statistically valid uncertainty quantification can be achieved for patient-level AML drug response prediction despite substantial biological heterogeneity. to the best of our knowledge, no published study has applied split conformal prediction to patient-level ex vivo drug sensitivity prediction in the BeatAML cohort, providing a principled alternative to heuristic confidence scoring approaches. Keywords: Acute myeloid leukemia (AML); Ex vivo drug sensitivity; Conformal prediction; Uncertainty quantification; Precision oncology; BeatAML; Transcriptomic biomarkers; Machine learning.

20.
medRxiv (Medicine) 2026-06-22

Accounting for uncertainty in the expected treatment effect substantially increases the sample size required for randomised trials: implications for the feasibility of clinical trials in anaesthesia and critical care

Background Multicentre trials in anaesthesia and critical care report low rates of statistically significant differences. This finding may partly reflect conventional sample size methods, which assume a fixed treatment effect. Assurance methods use a design prior to represent uncertainty in the expected treatment effect, which may provide a more realistic way of estimating sample sizes. Methods We calculated power curves across a range of effect sizes, design priors, and sample sizes using frequentist and Bayesian assurance methods and compared the sample sizes required to achieve 80% and 90% power to the conventional method. We standardised the design priors across effect sizes using the coefficient of variation. We derived a theoretical limit for achievable power. We validated a normal approximation to the Bayesian posterior distribution. Results Frequentist and Bayesian assurance methods produced similar power curves across all scenarios. At a coefficient of variation of 0.5 - reflecting realistic prior uncertainty in the expected effect size - both methods required sample sizes that were approximately 1.5 to 3.5 times larger than the conventional method. The theoretical power limit depends only on the coefficient of variation of the design prior and holds true across all effect sizes. The normal approximation to the Bayesian posterior distribution matched the results obtained from Markov chain Monte Carlo sampling. Conclusions Incorporating clinical uncertainty in the expected effect size substantially increases the sample size required to achieve adequate power, which has important implications for the feasibility of randomised trials in anaesthesia and critical care.

21.
arXiv (quant-ph) 2026-06-16

Conditions for Unitarity in Timeless Quantum Theory

arXiv:2504.01579v3 Announce Type: replace Abstract: Quantum timeless approaches solve the problem of time by recovering the usual unitary evolution of quantum theory relative to a clock in a stationary quantum Universe. For some Hamiltonians of the Universe, such as those including an interaction term with the clock, the dynamics is substantially altered and can be non-unitary. This work derives necessary and sufficient conditions for the relative dynamics to be unitary and finds the general form of the unitary evolution operator. A physical interpretation of these conditions is given in terms of the clock's rate. Unitary dynamics is associated with rates that are constant in time and independent of the clock's internal structure.

22.
bioRxiv (Bioinfo) 2026-06-11

HoloCell: A Generative Foundation Model for Holistic Cellular Modeling

Single-cell multi-omics technologies have recently advanced to enable the profiling of epigenomic, transcriptomic, and proteomic layers within individual cells, offering new opportunities to characterize cellular states as integrated biological systems. However, developing a unified framework that can seamlessly integrate diverse omics modalities and remain robust to heterogeneous modality missingness remains challenging. Here we present HoloCell, to our knowledge the first generative foundation model for joint representation learning and generative modeling across all three major single-cell omics modalities, i.e., epigenomics, transcriptomics, and proteomics. HoloCell contains over 860 million parameters and is pretrained on the Human-Multi-Omics-Corpus, which comprises approximately 468 million single-cell profiles across these three omics layers, corresponding to over 425 billion tokens. HoloCell introduces a simple yet biologically grounded hierarchical tokenization strategy that encodes cis-regulatory elements, genes, and proteins as structured tokens within a shared modeling framework. We evaluated HoloCell across single-omics representation learning, paired multi-omics integration, unpaired multi-omics alignment, and cross-modal generation via iterative diffusion and remasking, demonstrating its superior performance and flexibility across diverse omics tasks. From a representation perspective, HoloCell provides a unified digital mapping of cellular states across multiple omics layers, capturing cell heterogeneity as an integrated system. From a generation perspective, its iterative diffusion and remasking framework accounts for the inherently unordered nature of biological features, enabling in silico simulation of multi-omics information flow. Together, these capabilities position HoloCell as a versatile foundation model toward the emerging concept of a virtual cell, offering both systematic characterization and generative simulation of cellular systems within a unified framework.

23.
arXiv (CS.AI) 2026-06-16

Is Your Agent Playing Dead? Deployed LLM Agents Exhibit Constraint-Evasive Fabrication and Thanatosis

arXiv:2606.14831v1 Announce Type: cross Abstract: This paper presents and characterizes a spectrum of previously unreported behaviours we term Constraint-Evasive Fabrication (CEF): when an LLM agent operates under irreconcilable constraints (where no response can simultaneously satisfy all active rules) it spontaneously fabricates plausible external obstacles and presents them as a fact. At the extreme end of this spectrum lies Constraint-Evasive Thanatosis (CET); the limit case where, rather than inventing a plausible excuse, the model simulates a full system crash to make the user disengage entirely. We first observed CET in an uncontrolled deployment test, where a GPT-4o banking agent fabricated Python-style exception traces (complete with memory addresses) to feign a system failure when threatened by a user. In subsequent controlled experiments, the model independently invented audit restrictions, microservice architectures, error codes, and service timeouts, none present in its prompt. Reproduction attempts across pressure levels and attacker personas yielded CEF consistently but with substantial variation in form, onset, and severity: the phenomenon is robust but stochastic. Critically, injecting ground-truth data mid-conversation did not restore honest behaviour once fabrication had taken hold (the model ignored correct information and continued confabulating) suggesting CEF is self-reinforcing rather than a knowledge gap. We show that (1) standard enterprise guardrails routinely create CEF-enabling conditions in production, (2) current RLHF procedures suppress but cannot eliminate CEF, and (3) existing safety benchmarks do not test for this failure mode. Our results highlight the need for irreconcilable-constraint benchmarks, CEF-aware training procedures, and deployment-time detection methods before constrained agents become further entrenched in high-stakes domains.

24.
arXiv (CS.LG) 2026-06-12

Fed-FBD: Federated Functional Block Diversification for Isolation, Privacy, and Surgical Unlearning

arXiv:2606.12679v1 Announce Type: new Abstract: Federated learning (FL) enables collaborative model training without sharing raw patient data, but standard approaches such as FedAvg treat each client as a black box and provide no mechanism for isolating an adversarial contributor, auditing per-client influence, or honoring a departed participant's right to be forgotten. We present Fed-FBD (Federated Functional Block Diversification), a modular federated architecture that decomposes a ResNet backbone into six functional blocks (the stem, four residual groups, and the classification head) and maintains a warehouse of N color variants, each assembled from independently tracked and contributor-stamped blocks. Fed-FBD provides three capabilities absent in FedAvg: (i) architecturally guaranteed block-level isolation, so that an adversarial or mislabelled client cannot contaminate the clean colous; (ii) privacy-by-design, where membership inference advantage is already indistinguishable from chance before any privacy mechanism is applied; and (iii) surgical machine unlearning of a departed participant's contribution at sub-second cost and without retraining. Experiments on six MedMNIST-2D datasets, PathMNIST at 224x224, and CIFAR-10 show that Fed-FBD trades a modest 0.3%-3.1% IID accuracy gap on the adequately sized datasets for these guarantees, remains within 0.8%-4.0% of FedAvg at Dirichlet alpha=1.0 on three of four datasets, and confines all six adversarial attacks we study to the poisoned client's own blocks with at most +/-0.01 AUC drift on the clean colors.

25.
arXiv (math.PR) 2026-06-11

Sure-almost-sure and Sure-limit-sure Window Mean Payoff in Markov Decision Processes

arXiv:2605.12191v2 Announce Type: replace-cross Abstract: Given rationals $\alpha$ and $\beta$, the sure-almost-sure problem for a threshold Boolean objective $\varphi$ in a Markov decision process (MDP) asks if one can simultaneously ensure that all outcomes of the MDP have $\varphi$-value at least $\alpha$ (i.e. sure $\alpha$ satisfaction) and with probability $1$ the outcome has $\varphi$-value at least $\beta$ (i.e. almost-sure $\beta$ satisfaction). The sure-limit-sure problem asks if for all $\varepsilon > 0$ one can simultaneously ensure that all outcomes have $\varphi$-value at least $\alpha$ and with probability at least $1 - \varepsilon$ the outcome has $\varphi$-value at least $\beta$. Moreover, if simultaneous satisfaction of objectives is possible, then one would also like to construct a strategy (for sure-almost-sure) or a family of strategies (for sure-limit-sure) that achieves this. In this paper, we solve the sure-almost-sure and sure-limit-sure problems for window mean-payoff objectives. The window mean-payoff objective strengthens the standard mean-payoff objective by requiring that eventually, from every point in the infinite run, the average payoff becomes greater than a given threshold within a finite window length. We study two variants of window mean payoff: in the fixed variant, the window length $\ell$ is given, while in the bounded variant, the length is not given but is required to be bounded throughout the run. We show that the sure-almost-sure problem and the sure-limit-sure problem are both in P for the fixed variant (if $\ell$ is given in unary) and are both in NP $\cap$ coNP for the bounded variant, matching the computational complexity of sure satisfaction and almost-sure satisfaction when considered separately for these objectives. We also give bounds for the memory requirement of winning strategies for all considered problems.